The vigil in honor of 16-year-old Kimani Gray had been planned as an occasion for his grieving mother to address mourners and the media, but her remarks never happened. Instead, activists encouraged some of the 200 people to march towards the New York Police Department’s 67th Precinct, ending in dozens of arrests.

The teenager was fatally shot by two plainclothes police officers late Saturday night after he allegedly pointed a .38 caliber revolver at them. Police said the boy had been approached by the officers because he was behaving suspiciously and fiddling with his waistband — suggesting he was concealing a weapon. Family and friends of the teenager have disputed that he had a gun.

Joy Cutting, a family friend who said she had known Mr. Gray since birth, believed the autopsy showed the teen hadn’t been pointing a gun at the officers. “If he was trying to shoot the cops, they would have shot him in the front,” she said at the vigil.

Investigators determined Mr. Gray was struck once in the back of his left shoulder, once in back of each thigh, twice in the front right thigh, once in the left rib cage and once in the left forearm. A spokeswoman for the city’s chief medical examiner said the coroner was still investigating the details shooting.

Kevin Hagen for The Wall Street Journal

Police officers made an arrest.

Clergy leaders from the neighborhood and political officials didn’t participate in the march that splintered off from Wednesday night’s vigil, as a large number of teenagers moved west on Church Avenue. The march quickly turned chaotic, with groups of protesters breaking off and dashing into the streets.

What followed was hours of protesters’ clashing with police punctuated by arrests. At times, protesters threw bottles, bricks and chairs at police officers and police vehicles.

Two blocks east of the 67th Precinct, a young protester was seen throwing a brick through the back window of a police cruiser. An officer responded by using pepper spray a number of protesters.

A law-enforcement official said Thursday that the incident resulted in a total of 46 arrests, including three juveniles, mostly for disorderly conduct. Three police officers were injured and four police department vehicles were damaged.

One woman was also injured, telling police she had been hurt by participants in the protest, the official said. One reporter was hit by a projectile and received treatment at Kings County Hospital.

By 10:00 p.m., many of the protesters who had broken away returned to the vigil at 55th Street and Church Avenue. Tensions seemed to be decreasing until Mahnefah Gray, sister of the teen killed by police, was arrested while crossing the street. That touched off a new round of clashes, with protesters egging on police and officers responding with orange netting and more arrests.

“An officer grabbed her arm while she was crossing the street, and she jerked it to push him away,” said Anthony Barnwell, 21, who identified himself as a cousin. “Then three cops grabbed her and slammed her on the ground.”

Associated Press

Memorial candles stand beside a picture of Kimani Gray during a vigil for the deceased teen

City Councilman Jumaane Williams, who had helped organized the vigil and tried throughout the night to deescalate the confrontations between protesters and police, took to Twitter to criticize those he felt had instigated the rampage. Mr. Williams tweeted that he was “furious at adults from OUTSIDE the community who incite our angry young people!!! You do not help and not wanted if you bring destruction!”

Anger over Mr. Gray’s killing had also been evident late Monday, when a group of about 40 people splintered from a previous vigil to confront police. The rampage damaged several businesses, including a raid on a local Rite-Aid store, as well as at least one city bus and passing cars.